Future of Data Sharing

The Future of Data Sharing Platforms in Academic MedicineA Basic Science Perspective
Philip E. Bourne
University of California San Diego
pbourne@ucsd.edu
Nov. 4, 2010
Physician Scientist Careeer Development
http://www.slideshare.net/pebourne/jim-gray-award-lecture

Why Am I Here?
I am a practicing basic life scientist who is concerned about the speedof dissemination and level of comprehension in an eScience world
I am fortunate enough to have a major biological resource (the Protein Data Bank) and a major biological journal (PLoS Computational Biology) as my playground for experimenting how we might do better
It is your engagement that will facilitate change
I believe your ability to embrace these changes will impact your career
Nov. 4, 2010

The Scientific Process is Too Slow to Respond to a Crisis – Either Global or Personal
Nov. 4, 2010
By the time the paper is published
we could all be dead
http://knol.google.com/k/plos-currents-influenza#
Motivation

In a time of crisis the need for fast access
to accurate data and any knowledge of
that data are paramount
Structure Summary page activity for
H1N1 Influenza related structures
Jan. 2008
Jan. 2009
Jan. 2010
Jul. 2009
Jul. 2008
Jul. 2010
3B7E: Neuraminidase of A/Brevig Mission/1/1918
H1N1 strain in complex with zanamivir
1RUZ: 1918 H1 Hemagglutinin
* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm
Motivation
Nov. 4, 2010

If that is not enough…For some people the scientific process may be too slow to save their life
Nov. 4, 2010
Motivation

Josh Sommer – A Remarkable Young ManCo-founder & Executive Director the Chordoma Foundation
Nov. 4, 2010
http://sagecongress.org/Presentations/Sommer.pdf
Motivation

Chordoma
A rare form of brain cancer
No known drugs
Treatment – surgical resection followed by intense radiation therapy
Nov. 4, 2010
http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
Motivation

Nov. 4, 2010
Motivation

Nov. 4, 2010
If I have seen further it is only by
standing on the shoulders of giants
Isaac
Isaac Newton
From Josh’s point of view the climb
up just takes too long
> 15 years and > $850M to be
more precise
Adapted: http://sagecongress.org/Presentations/Sommer.pdf
Motivation

Nov. 4, 2010
Motivation

Nov. 4, 2010
http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation
Motivation

Now we are all hopefully motivated let us break this down to what actually needs to be done in my opinion Here are a few big things …
Nov. 4, 2010

A Few Things to Accelerate the Rate of Scientific Discovery
A commitment to greater openness
Improved characterization (i.e. metadata including provenance) and persistence of data
A change in the reward system
Seamless integration between the data and the knowledge derived from that data
Better management of the digital scientific workflow
Unleash the full power of the Internet
Nov. 4, 2010

We Need Data and Knowledge About That Data to Interoperate
The Knowledge and Data Cycle
0. Full text of PLoS papers stored
in a database
4. The composite view has
links to pertinent blocks
of literature text and back to the PDB
User clicks on content
Metadata and webservices to data provide an interactiveview that can be annotated
Selecting features provides a data/knowledge mashup
Analysis leads to new content I can share
4.
1.
3. A composite view of
journal and database
content results
1. A link brings up figures
from the paper
3.
2.
2. Clicking the paper figure retrieves
data from the PDB which is
analyzed
PLoS Comp. Biol. 2005 1(3) e34
Nov. 4, 2010

Seamless Integration Between the Data and the Knowledge Derived from that Data – What is Stopping US?
Technology - NO
STM publishers - Yes
Funding agencies - Yes
You - ???
Nov. 4, 2010

The Publishers are Starting to Do It
Nov. 4, 2010
From Anita de Waard, Elsevier

Nov. 4, 2010

Reward Systems Need to ChangeWhat is Needed?
Author disambiguation
Auditing (identification and metrics) of all scholarship - means new tools
Seniors need to promote alternative forms of scholarship
Juniors need to respond to it
Nov. 4, 2010
Ten Simple Rules for Getting Promoted as a Computational Biologist in Academia
PLoS Comp Biol to appear Nov. 2010
Reward Systems Need to Change

Example Tools
Nov. 4, 2010
http://www.researcherid.com/
http://pubnet.gersteinlab.org/
http://www.biomedexperts.com

What Are these Alternative Forms of Scholarship?
Reviews
Curation
Research
[Grants]
Journal
Article
Poster
Session
Conference
Paper
Blogs
Community Service/Data
Nov. 4, 2010

Nov. 4, 2010

A Unique Identifier is Going to Happen
It is DOIs for people
Some scientists will resist
The winner is ORCHID?
Nov. 4, 2010
I an Not a Scientist I am a Number
PLoS Comp. Biol. 2008 4(12) e1000247

Ideally the ID will be Tagged to Every Piece of Scholarly Communication
I an Not a Scientist I am a Number
PLoS Comp. Biol. 2008 4(12) e1000247
Nov. 4, 2010

Nov. 4, 2010

Yes YouTube Can Increase the Rate of Discovery
Nov. 4, 2010

The Lab ExperimentPaper+Rich Media
My students enjoyed the experience
The shyest student was actually the most bold in front of the camera
“We will become a generation of “science castors”
They liked the exposure for the most part – rather than the PI it puts them out in front
Nov. 4, 2010

What Emerged: SciveeCasts
Products
ApplicationProductPrimary Customers
Journals PubCastJournals, publishers, societies
Meetings PosterCast Societies, conference orgs.
SlideCast
Comm. PaperCast Societies, journals
Podcast
SlideCast
Education PosterCast Societies, universities
SlideCast
BooksBookCast Publishers, book sellers
Nov. 4, 2010

The Promise – A Hypothetical Example
Cardiac Disease
Literature
Immunology Literature
Shared Function
Nov. 4, 2010

Acknowledgements
BioLit Team
Lynn Fink
Parker Williams
Marco Martinez
RahulChandran
Greg Quinn
MBT
John Moreland
John Beaver
Microsoft Scholarly Communications
Pablo Fernicola
Lee Dirks
SavasParastitidas
Alex Wade
Tony Hey
wwPDB team
Andreas Prilc
DimitrisDimitropoulos
SciVee Team
Apryl Bailey
Leo Chalupa
Lynn Fink
Marc Friedman (CEO)
Ken Liu
Alex Ramos
Willy Suwanto
Ben Yukich
http://www.scivee.tv
http://biolit.ucsd.edu
http//www.pdb.org
http://www.codeplex.com/ucsdbiolit
Nov. 4, 2010

pbourne@ucsd.edu
Questions?
Nov. 4, 2010
http://www.slideshare.net/pebourne/jim-gray-award-lecture

Future of Data Sharing

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